Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

Abstract

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first “metagenomic snapshots” of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a “salt-in” strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.

Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency

“…In addition, establishing the connection between microbial diversity and physiological functions, that is, who is doing what, constitutes a fundamental problem (Maron et al, 2008; Prosser, 2015). Streit and Schmitz (2004) declared that metagenomics might be the key to investigating uncultured microbes (Vavourakis et al, 2016). Although the newly developed single-cell sequencing approach provides a method to obtain insights into uncultured microbes efficiently (Rinke et al, 2013), metagenomic library based method is cost-effective and enables high-throughput identification of organismal communities from small amounts of DNA (Williams et al, 2014).…”

Three novel bacteriophages isolated from the East African Rift Valley soda lakes

“…Two soda lake metagenome datasets (Kulunda Steppe Russia and Soda Lake California) are currently available and these were investigated for the presence of the phages described here [65] (SRR3306837). From the Soda lake metagenomic dataset 111 reads mapped to the Shpa genome at 80% similarity and 60% length fraction or reads, covering 2771 bp of the genome, and 34 reads mapped to Shbh1.…”

Diversity and Distribution of Phenol Oxidase Producing Fungi from Soda Lake and Description of Curvularia lonarensis sp. nov.

“…Furthermore, detection of active enzyme secretion in extreme conditions (high pH and salinity) indicates their probable role in the degradation of complex organics like leaf-litter, plant debris and detoxification of phenolics present in lake ecosystem and contribution in carbon turnover of the lake. Recently, Vavourakis et al (2016) and Ausec et al (2011) have shown in metagenomic studies of various soda lake that many uncultured fungi have laccases-like Cu-oxidase encoded which may be involved in degradation of phenolic compounds. Hence, this is the first culture based study on Soda lake showing phenolic compound degradation capacities of fungal isolates from such habitat.…”